smriprep
Package Info
SMRIPrep: a structural MRI data preprocessing pipeline including Freesurfer
Required licenses
Name | URL | Description |
---|
freesurfer | https://surfer.nmr.mgh.harvard.edu/registration.html | sMRIPRep uses FreeSurfer tools, which require a license to run. |
Command
Key | Value |
---|
Task | arcana.bids:bids_app |
Operates on | session |
Name | Required data-type | Default column data-type | Description |
---|
T1w | medimage/nifti-gz-x | medimage/dicom-series | T1-weighted anatomical scan |
T2w | medimage/nifti-gz-x | medimage/dicom-series | T2-weighted anatomical scan |
Outputs
Name | Required data-type | Default column data-type | Description |
---|
smriprep | generic/directory | generic/directory | Preprocessed sMRI data |
Parameters
Name | Data type | Description |
---|
smriprep_flags | str | Command line flags passed on directly to sMRIPrep |
json_edits | str | JQ filters (https://devdocs.io/jq/) to apply to JSON side-cars in order to handle special cases where the dcm2niix fails to produce valid a BIDS |